Variant report

Variant	rs7284538
Chromosome Location	chr22:30375534-30375535
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30366853..30371460-chr22:30371891..30375827,4	MCF-7	breast:
2	chr22:30369409..30372830-chr22:30374993..30377919,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100330	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs12373962	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12484336	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12485243	1.00[CEU][hapmap];0.87[GIH][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes]
rs16987156	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16988084	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16988135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28428766	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28522206	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28595572	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3788421	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57462999	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57653653	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61352751	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7285751	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7286551	0.85[AMR][1000 genomes]
rs7286905	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7290085	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7292732	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73161050	0.81[AMR][1000 genomes]
rs73161074	0.83[AMR][1000 genomes]
rs73161099	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73162731	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73162773	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73883345	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8138677	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8139217	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8140366	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8140770	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9306466	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9608822	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9608823	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9608836	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9608843	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9608845	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9614063	0.81[AMR][1000 genomes]
rs9614071	0.87[AMR][1000 genomes]
rs9614075	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9614083	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9614087	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9614089	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9614097	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9614101	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9614105	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9614108	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9614109	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9614110	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9614111	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9614122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614124	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614127	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614128	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9614129	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614131	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614132	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9614143	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9614144	0.92[CEU][hapmap];0.83[CHB][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes]
rs9614145	0.85[AMR][1000 genomes]
rs9680595	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9680809	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9983	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv523696	chr22:30326102-30381789	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv3591	chr22:30344208-30388897	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7284538	MTMR3	cis	Artery Tibial	GTEx
rs7284538	INPP5J	cis	cerebellum	SCAN
rs7284538	MTMR3	cis	lung	GTEx
rs7284538	MTMR3	cis	multi-tissue	Pritchard
rs7284538	MTMR3	cis	Nerve Tibial	GTEx
rs7284538	MTMR3	Cis_1M	lymphoblastoid	RTeQTL
rs7284538	MTMR3	cis	Thyroid	GTEx
rs7284538	MTMR3	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30340800-30376000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr22:30344400-30376000	Weak transcription	HSMMtube	muscle
3	chr22:30344600-30375600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr22:30345400-30379000	Weak transcription	Esophagus	oesophagus
5	chr22:30348400-30387200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr22:30350600-30402600	Weak transcription	Aorta	Aorta
7	chr22:30351200-30385800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr22:30351200-30387400	Weak transcription	Ovary	ovary
9	chr22:30352800-30388600	Weak transcription	HepG2	liver
10	chr22:30354600-30390200	Weak transcription	Colonic Mucosa	Colon
11	chr22:30354800-30390400	Weak transcription	Small Intestine	intestine
12	chr22:30356200-30376600	Weak transcription	Fetal Kidney	kidney
13	chr22:30358800-30387400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr22:30359400-30375600	Weak transcription	Fetal Lung	lung
15	chr22:30363200-30375600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr22:30363400-30427800	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr22:30366000-30384200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr22:30366400-30387400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr22:30366600-30390800	Weak transcription	Gastric	stomach
20	chr22:30366800-30375600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr22:30366800-30376000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr22:30367000-30375600	Weak transcription	Colon Smooth Muscle	Colon
23	chr22:30367000-30426600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr22:30367400-30397800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr22:30368400-30382800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr22:30368400-30387400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr22:30369400-30382600	Weak transcription	Brain Anterior Caudate	brain
28	chr22:30369400-30388400	Weak transcription	NH-A	brain
29	chr22:30370000-30391000	Weak transcription	Fetal Heart	heart
30	chr22:30370200-30388400	Weak transcription	NHLF	lung
31	chr22:30370600-30390800	Weak transcription	Right Ventricle	heart
32	chr22:30370800-30379400	Weak transcription	HSMM	muscle
33	chr22:30370800-30387400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr22:30370800-30390000	Weak transcription	Stomach Mucosa	stomach
35	chr22:30371000-30375600	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr22:30371000-30383200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr22:30371200-30382000	Weak transcription	Brain Substantia Nigra	brain
38	chr22:30371800-30375600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr22:30371800-30385800	Weak transcription	Lung	lung
40	chr22:30371800-30386600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr22:30372600-30377800	Strong transcription	Fetal Muscle Leg	muscle
42	chr22:30373400-30383000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr22:30373400-30388600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr22:30373600-30377600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr22:30373600-30377800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr22:30373600-30383400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr22:30373600-30383600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr22:30373600-30388600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr22:30373800-30377600	Strong transcription	Primary B cells from peripheral blood	blood
50	chr22:30373800-30391400	Strong transcription	Primary T helper cells fromperipheralblood	blood

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